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- PDB-3t4z: Crystal Structure of NaK2K Channel Y55W Mutant -

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Basic information

Entry
Database: PDB / ID: 3t4z
TitleCrystal Structure of NaK2K Channel Y55W Mutant
ComponentsPotassium channel protein
KeywordsMEMBRANE PROTEIN / Ion Channel
Function / homology
Function and homology information


potassium channel activity / metal ion binding / identical protein binding / membrane
Similarity search - Function
Two pore domain potassium channel / Helix Hairpins - #70 / Potassium channel domain / Ion channel / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
: / Potassium channel protein
Similarity search - Component
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.901 Å
AuthorsSauer, D.B. / Zeng, W. / Raghunathan, S. / Jiang, Y.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Protein interactions central to stabilizing the K+ channel selectivity filter in a four-sited configuration for selective K+ permeation.
Authors: Sauer, D.B. / Zeng, W. / Raghunathan, S. / Jiang, Y.
History
DepositionJul 26, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2011Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Potassium channel protein
B: Potassium channel protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,90210
Polymers21,5892
Non-polymers3138
Water66737
1
A: Potassium channel protein
hetero molecules

A: Potassium channel protein
hetero molecules

A: Potassium channel protein
hetero molecules

A: Potassium channel protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,80420
Polymers43,1794
Non-polymers62616
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area8920 Å2
ΔGint-62 kcal/mol
Surface area16820 Å2
MethodPISA
2
B: Potassium channel protein
hetero molecules

B: Potassium channel protein
hetero molecules

B: Potassium channel protein
hetero molecules

B: Potassium channel protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,80420
Polymers43,1794
Non-polymers62616
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area8960 Å2
ΔGint-63 kcal/mol
Surface area17810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.388, 68.388, 86.520
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4
Components on special symmetry positions
IDModelComponents
11A-1-

K

21A-2-

K

31A-3-

K

41A-4-

K

51B-5-

K

61B-6-

K

71B-7-

K

81B-8-

K

91B-12-

HOH

101B-13-

HOH

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Components

#1: Protein Potassium channel protein


Mass: 10794.709 Da / Num. of mol.: 2 / Mutation: Y55W, D66Y, N68D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (bacteria) / Strain: ATCC 14579 / DSM 31 / Gene: BC_0669 / Plasmid: pQE60 / Production host: Escherichia coli (E. coli) / Strain (production host): SG13009 / References: UniProt: Q81HW2
#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: K
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 47.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 65% MPD, 100mM Glycine, pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9790983 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 22, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9790983 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. obs: 14653 / Observed criterion σ(I): 1.13
Reflection shell
Resolution (Å)Diffraction-ID% possible all
1.9-1.93174.5
1.93-1.97184
1.97-2.01184.4
2.01-2.05186.5
2.05-2.09188.9
2.09-2.14189.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.6.1_357)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.901→28.835 Å / SU ML: 0.21 / σ(F): 1.37 / Phase error: 34.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2415 727 5.03 %Random
Rwork0.2258 ---
obs0.2265 14444 92.15 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 101.874 Å2 / ksol: 0.367 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--18.7698 Å2-0 Å20 Å2
2---18.7698 Å2-0 Å2
3---37.5395 Å2
Refinement stepCycle: LAST / Resolution: 1.901→28.835 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1489 0 8 37 1534
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031527
X-RAY DIFFRACTIONf_angle_d0.732084
X-RAY DIFFRACTIONf_dihedral_angle_d11.361520
X-RAY DIFFRACTIONf_chiral_restr0.046259
X-RAY DIFFRACTIONf_plane_restr0.003250
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.901-2.04810.381090.36582263X-RAY DIFFRACTION76
2.0481-2.25410.31611580.31682663X-RAY DIFFRACTION90
2.2541-2.58010.24521570.24822850X-RAY DIFFRACTION97
2.5801-3.250.23911560.17922978X-RAY DIFFRACTION99
3.25-28.83880.20831470.20672963X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.6141-0.2347-0.19620.87340.10140.6474-0.0187-0.0403-0.36990.0952-0.10710.03510.250.04020.13920.4037-0.02020.05980.36950.05730.6017-0.8714-13.161223.4019
21.16920.4477-0.28041.31930.54920.3290.0995-0.1827-0.17620.02550.0160.33540.1579-0.1523-0.00760.4084-0.00790.09140.38870.00880.4522-11.4108-6.8895-21.1356
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B

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